Description
A CBS object holds results from the
Circular Binary Segmentation (CBS) method
for one sample for one or more chromosomes.
Package: PSCBS
Class CBS
list
~~|
~~+--AbstractCBS
~~~~~~~|
~~~~~~~+--CBS
Directly known subclasses:
public abstract static class CBS
extends AbstractCBSFields and Methods
Methods:
rll{
append Appends one segmentation result to another.
as -
estimateStandardDeviation Estimates the whole-genome standard deviation of the signals.
getSegmentSizes -
plotTracks Plots copy numbers along the genome.
pruneBySdUndo Prune the CBS profile by dropping change points that are too small.
segmentByCBS -
writeSegments Writes the table of segments to file.
}
Methods inherited from AbstractCBS:
all.equal, append, as.data.frame, drawChangePoints, dropChangePoint, dropChangePoints, dropRegion, dropRegions, extractChromosome, extractChromosomes, extractCNs, extractRegions, extractSegments, getChromosomes, getLocusData, getSampleName, getSegments, getSegmentSizes, load, mergeThreeSegments, mergeTwoSegments, nbrOfChangePoints, nbrOfChromosomes, nbrOfLoci, nbrOfSegments, plotTracks, print, pruneByHClust, renameChromosomes, resegment, sampleCNs, sampleName, sampleName<-, save, setLocusData, setSampleName, setSegments, tileChromosomes, updateMeans
Methods inherited from list:
all.equal, as.data.frame, attachLocally, callHooks, relist, withinDifference to DNAcopy object
A CBS object is similar to DNAcopy objects with the major
difference that a CBS object holds only one sample, whereas
a DNAcopy object can hold more than one sample.See also
The segmentByCBS() method returns an object of this class.